add tag regex for file of lanes
specify pathogens gcdepth R script for QC
Merge pull request #38 from andrewjpage/gc_depth

specify pathogens gcdepth R script for QC
added config length filtering default and update assembly version number
Merge pull request #39 from martinghunt/update_assembly_pipeline_version

added config length filtering default and update assembly version number
added tests for --smalt_mapper_l
added --smalt_mapper_l parameter
updated help text
updated error message
Merge pull request #35 from CraigPorter/fix_file_of_lanes

add tag regex for file of lanes
Merge pull request #40 from CraigPorter/add_pairtype_option_for_smalt

Add pairtype option for smalt